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fix: robust timeout and patch split param #14

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fix: robust timeout and patch split param #14

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flashlab
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@flashlab flashlab commented Mar 8, 2023

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@flashlab flashlab mentioned this pull request Mar 8, 2023
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mihailefter
mihailefter reviewed Mar 13, 2023
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Why do you need the timeout default value changed? It can be configured via the CLI or from the function call.

mutalyzer_retriever/cli.py
@@ -106,6 +106,10 @@ def _parse_args(args):
"--ref_id_start", help="reference id should start with"
)

parser_ncbi_assemblies.add_argument(
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This is already added above at line 70.

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Actually I can't use --split in ncbi_assemblies subcommand like mutalyzer_retriever ncbi_assemblies --input downloads/ --ref_id_start NC_000011 --downloaded --split

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You can make use of the following: mutalyzer_retriever --split ncbi_assemblies --input downloads/ --ref_id_start NC_000011 --downloaded.

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Why do you need the timeout default value changed? It can be configured via the CLI or from the function call.

Sorry, I missed timeout argument since it's not in the document. I'll close the pull request.
But the question still remains, why the program failed to extract exon and transcript feature from some kind of reference like NC_000011.9(GRCH37). Seems same issue in #12.

@flashlab flashlab closed this Mar 15, 2023
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